Help:References

CAZypedia uses the Biblio extension for creating in-text citations and a reference list. Full details about Biblio can be found at the Biblio homepage. The following is a succinct set of instructions for using Biblio with CAZypedia.

The basics

Biblio uses two types of tags to format references. The first is the <cite>...</cite> pair of tags, which specify where a reference should be placed in the text. Within these tags, one places a reference code that points to an entry in the bibliography, specified within the <bibilo>...</biblio> tags.

Example CAZypedia code would look like this:

'''Main text'''
The first structure of a GH1 enzyme was solved in 1995 <cite>REF1</cite>.
Stryer wrote a book about biochemistry <cite>stryertext</cite>.

'''Reference list'''
<biblio>
#REF1 Barrett T, et al. Structure 1995 Sep 15; 3(9) 951-60.
#stryertext Berg, Tymoczko, & Stryer. Biochemistry. New York: W.H. Freeman, 2002.
</biblio>

Which would give this on the actual CAZypedia page:

Main text The first structure of a GH1 enzyme was solved in 1995 [1]. Stryer wrote a book about biochemistry [2]. Reference list Barrett T, et al. Structure 1995 Sep 15; 3(9) 951-60. Berg, Tymoczko, & Stryer. Biochemistry. New York: W.H. Freeman, 2002.

Note that:

• The reference code can be whatever you want (e.g.: REF1, stryertext)
• Whatever follows the reference code is placed verbatim into the reference list - you can put any text here, with any formatting you want.
• Biblio can also insert full citations for you, for those references which have a PubMed ID or an ISBN (see below).

Citing works using PubMed IDs and ISBNs

One very slick feature of Biblio is that it can retrive entire references directly from PubMed or a ISBN server. That means you can just enter the PubMed ID (pmid) or ISBN directly after the reference code, and CAZypedia will do the rest for you.

The code for our previous example would then look like this:

'''Main text:'''

The first structure of a GH1 enzyme was solved in 1995 <cite>REF1</cite>.
Stryer wrote a book about biochemistry <cite>stryertext</cite>.

'''Reference list:'''
<biblio>
#REF1 pmid=8535788
#stryertext isbn=0-7167-4954-8
</biblio>

Which would give this on the CAZypedia page:

Main text: The first structure of a GH1 enzyme was solved in 1995 [1]. Stryer wrote a book about biochemistry [2]. Reference list: Barrett T, Suresh CG, Tolley SP, Dodson EJ, and Hughes MA. (1995). The crystal structure of a cyanogenic beta-glucosidase from white clover, a family 1 glycosyl hydrolase. Structure. 1995;3(9):951-60. DOI:10.1016/s0969-2126(01)00229-5 |

Note here that all the references are automatically linked to various external web sources.

Using EndNote for formatting references in CAZypedia

It is anticipated that many CAZypedia editors will be regular users of the reference management software EndNote. EndNote can be used to both insert the in-text citations (e.g. <cite>REF1</cite> and format content to go in the <biblio>...</bibilo> tags.

The following is a step-by-step guide to using EndNote with MS Word in Windows to format text to cut and paste into CAZypedia.

Download the CAZypedia EndNote style, CAZypedia.ens, from this link (http://www.biotech.kth.se/cazypedia/CAZypedia.ens) and save the file in your EndNote styles folder (e.g. C:\Program Files\EndNote 9\Styles). Write your CAZypedia entry in MS Word, inserting references via EndNote as usual. Format your entry using the CAZypedia style (CAZypedia.ens) Note that all references in the bibliography will now start with "#N, where N is the reference number and that these numbers will be referenced in the text with <cite>N</cite>. Save your Word file with an informative field name such as CAZypediaText.doc Select all of your text + references by pressing Ctrl+A (Windows) With everything selected, press Ctrl+6 to remove all EndNote "field codes." Save this version as a Word new file, e.g. CAZypediaText_NoFields.doc Copy and paste your main text into a CAZypedia page edit window. Copy and paste your bibliography under a heading titled References. Add the tag <biblio> before the bibliography. Add the tag </biblio> after the bibliography. Preview and save your entry.

This procedure will work best when writing a page from scratch. Be very careful when adding text to a page that reference codes are not used more than once in the bibliography. (You can cite a reference as much as you like in the text.)

Using EndNote to format references with PubMed IDs and ISBNs

It should be possible to combine the above two methods for building a bibliography and referencing it in the text. This would require:

• PubMed IDs or ISBNs must be added in fields in your EndNote records.
• The CAZypedia EndNote style must be altered to output bibliographic records in the format "#refN pmid=nnnnnnn" and "#refN isbn=yyyyyyyyyy"

Since this depends on how CAZypedia editors add PubMed IDs and ISBNs to their EndNote libraries, no general solution can be given.